Blender 2.81: How do I import the rig correctly?
I don't know why exactly this is happening (I'm using 2.82a and having the same issue), but since you have so few bones which are misaligned, I find that I was able to go into Edit Mode and manually adjust them in less than five minutes. 

Regretably, this is not the answer you were hoping for. But it seems to work.